Metafounder approach for single-step genomic evaluations of Red Dairy cattle
| Autor: | Andrei A. Kudinov, Esa Mäntysaari, Ismo Strandén, Gert Pedersen Aamand, Pekka Uimari |
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| Přispěvatelé: | Animal Science Research, Department of Agricultural Sciences, Helsinki One Health (HOH) |
| Rok vydání: | 2020 |
| Předmět: |
Male
LINKAGE DISEQUILIBRIUM Genotype PHASE education Pedigree chart Best linear unbiased prediction GENETIC EVALUATION 03 medical and health sciences Matrix (mathematics) Gene Frequency HOLSTEIN Statistics Linear regression Genetics Animals 412 Animal science dairy science Allele frequency 030304 developmental biology Mathematics Food Formulated UNKNOWN-PARENT GROUPS 0303 health sciences Genome Models Genetic PERSISTENCE 0402 animal and dairy science Reproducibility of Results Genomics 04 agricultural and veterinary sciences 040201 dairy & animal science Breed Pedigree MODEL Minor allele frequency BIAS POPULATIONS Cattle Female Animal Science and Zoology Purebred Selective Breeding Food Science |
| Zdroj: | Journal of Dairy Science. 103:6299-6310 |
| ISSN: | 0022-0302 |
| Popis: | Single-step genomic BLUP (ssGBLUP) is a powerful approach for breeding value prediction in populations with a limited number of genotyped animals. However, conflicting genomic (G) and pedigree (A22) relationship matrices complicate the implementation of ssGBLUP into practice. The metafounder (MF) approach is a recently proposed solution for this problem and has been successfully used on simulated and real multi-breed pig data. Advantages of the method are easily seen across breed evaluations, where pedigrees are traced to several pure breeds, which are thereafter used as MF. Application of the MF method to ruminants is complicated due to multi-breed pedigree structures and the inability to transmit existing unknown parent groups (UPG) to MF. In this study, we apply the MF approach for ssGBLUP evaluation of Finnish Red Dairy cattle treated as a single breed. Relationships among MF were accounted for by a (co)variance matrix (Γ) computed using estimated base population allele frequencies. The attained Γ was used to calculate a relationship matrix A 22 Γ for the genotyped animals. We tested the influence of SNP selection on the Γ matrix by applying a minor allele frequency (MAF) threshold (ΓMAF) where accepted markers had an MAF ≥0.05. Elements in the ΓMAF matrix were slightly lower than in the Γ matrix. Correlation between diagonal elements of the genomic and pedigree relationship matrices increased from 0.53 (A22) to 0.76 ( A 22 Γ and A 22 Γ MAF ). Average diagonal elements of A 22 Γ and A 22 Γ MAF matrices increased to the same level as in the G matrix. The ssGBLUP breeding values (GEBV) were solved using either the original 236 or redefined 8 UPG, or 8 MF computed with or without the MAF threshold. For bulls, the GEBV validation test results for the 8 UPG and 8 MF gave the same validation reliability (R2; 0.31) and over-dispersion (0.73, measured by regression coefficient b1). No significant R2 increase was observed in cows. Thus, the MF greatly influenced the pedigree relationship matrices but not the GEBV. Selection of SNP according to MAF had a notable effect on the Γ matrix and made the A22 and G matrices more similar. |
| Databáze: | OpenAIRE |
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